Proteomics has moved beyond the cataloguing of proteins towards the quantification of proteomic changes between two or more conditions. These proteomic changes may be quantified using a traditional shotgun analysis or using a more targeted mass spectrometry (MS) analysis such as single reaction monitoring (SRM), multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM). Targeted MS analyses require proteotypic peptides that are reproducibly selected in each analysis. For a peptide to be considered proteotypic, it needs to be observable by mass spectrometry. In addition, it needs to be unique for the protein it is representing, and ideally without post-translational or chemically induced modifications. The general recommendation is also to avoid peptides that contain methionines since methionines are prone to oxidation.
However, these conditions imposed on proteotypic peptides limit the applicability of targeted analyses when a biological study requires the analysis of a peptide that contains a methionine or may be post-translationally modified. There are a substantial number of methionine-containing peptides that are important in biological studies. An example of a methionine-containing peptide includes TAGTSFMMTPYVVTR (SEQ ID NO: 1) from c-jun N-terminal kinase-1 or GAILTTMLATR (SEQ ID NO: 2) from Ca2+/calmodulin-dependent protein kinase II (CaMKII), which is known to be modulated during memory and learning, and thus, it is more effective and efficient if they can be quantified when studied in this context. To study methionine-containing peptides, they would have to be monitored in their oxidized and reduced forms. If additional post-translational modifications are to be studied, the number of necessary transitions quickly increases.